GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pseudomonas stutzeri RCH2

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate GFF1678 Psest_1716 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__psRCH2:GFF1678
          Length = 253

 Score =  152 bits (384), Expect = 7e-42
 Identities = 93/262 (35%), Positives = 138/262 (52%), Gaps = 13/262 (4%)

Query: 1   MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60
           MS  F+G+V LVTGA   IG ATA   AE+G  + L D++   +     S+R  G EA +
Sbjct: 1   MSMTFSGQVALVTGAAAGIGRATAQAFAEQGLKVVLADIDEAGIRDGAESIRAAGGEAIA 60

Query: 61  YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120
             CDVT +  V   ++ V+  FG++D+ FNNAG +     + +    +F  ++ +NV G 
Sbjct: 61  VRCDVTRDAEVKALIEQVLAQFGRLDYAFNNAGIEIEQGRLAEGSEAEFDAIMGVNVKGV 120

Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180
           +  +K     M+ Q  G IVNTAS+AG+   P M+ Y  SK A+I LT++AA++ A   I
Sbjct: 121 WLCMKHQLPVMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYAKKKI 180

Query: 181 RVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGV 240
           RVNA+ P  +    M+ R  E            DP+  A+      P+ R G + EI   
Sbjct: 181 RVNAVCPAVIDTD-MFRRAYE-----------ADPR-KAEFAAAMHPVGRIGKVEEIAAA 227

Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262
           V +L  D ++F TG  L + GG
Sbjct: 228 VLYLCCDGAAFTTGQALAVDGG 249


Lambda     K      H
   0.318    0.135    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 142
Number of extensions: 4
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 262
Length of database: 253
Length adjustment: 24
Effective length of query: 238
Effective length of database: 229
Effective search space:    54502
Effective search space used:    54502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory